A cause or origin; the seed/source of something. The reading 'kusa' (or colloquially 'gusa') is archaic or dialectal and occurs in compounds/phrases.
そんな小さな誤解が争いの種になった。
Such a small misunderstanding became the seed of the dispute.
彼の嫉妬が問題の種だったと後で分かった。
We later realized his jealousy was the root cause of the problem.
A variety or kind (a type). In modern usage '種類' or '品種' are more common.
この花にはいくつかの種がある。
This flower has several varieties.
果物売り場ではリンゴが五種並んでいた。
At the fruit stall five kinds of apples were lined up.
Used as a counter for varieties — as in the form '〜種' to count the number of different types/items.
この店ではジャムが三種（さんしゅ）売られている。
Three varieties of jam are sold at this shop.
展示された陶器は十種に分類されている。
The displayed pottery is classified into ten types.